• Ancient and modern genomes unravel the evolutionary history of the rhinoceros family 

      Liu, Shanlin; Westbury, Michael V; Dussex, Nicolas; Mitchell, Kieren J.; Sinding, Mikkel-Holger S.; Heintzman, Peter D.; Duchêne, David A.; Kapp, Joshua D.; von Seth, Johanna; Heiniger, Holly; Sánchez-Barreiro, Fatima; Margaryan, Ashot; André-Olsen, Remi; De Cahsan, Binia; Meng, Guanliang; Yang, Chentao; Chen, Lei; van der Valk, Tom; Moodley, Yoshan; Rookmaaker, Kees; Bruford, Michael W.; Ryder, Oliver; Steiner, Cynthia; Bruins-van Sonsbeek, Linda G. R.; Vartanyan, Sergey; Guo, Chunxue; Cooper, Alan; Kosintsev, Pavel; Kirillova, Irina V.; Lister, Adrian M.; Marques-Bonet, Tomas; Gopalakrishnan, Shyam; Dunn, Robert R.; Lorenzen, Eline D.; Shapiro, Beth; Zhang, Guojie; Antoine, Pierre-Olivier; Dalén, Love; Gilbert, Marcus Thomas Pius (Peer reviewed; Journal article, 2021)
      Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct ...
    • Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing 

      Mak, Sarah S.T.; Gopalakrishnan, Shyam; Carøe, Christian; Geng, Chunyu; Liu, Shanlin; Sinding, Mikkel Holger Strander; Kuderna, Lukas FK; Zhang, Wenwei; Fu, Shujin; Vieira, Filipe G.; Germonpre, Mietje; Bocherens, Hervé; Fedorov, Sergey; Petersen, Bent; Sicheritz-Pontén, Thomas; Marques-Bonet, Tomas; Zhang, Guojie; Jiang, Hui; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2017)
      Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant ...
    • Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet 

      Gelabert, Pere; Sandoval-Velasco, Marcela; Serres, Aitor; de Manuel, Marc; Renom, Pere; Margaryan, Ashot; Stiller, Josefin; De-Dios, Toni; Fang, Qi; Feng, Shaohong; Mañosa, Santi; Pacheco, George; Ferrando-Bernal, Manuel; Shi, Guolin; Hao, Fei; Chen, Xianqing; Petersen, Bent; Olsen, Remi-André; Navarro, Arcadi; Deng, Yuan; Dalén, Love; Marques-Bonet, Tomas; Zhang, Guojie; Antunes, Agostinho; Gilbert, Marcus Thomas Pius; Lalueza-Fox, Carles (Peer reviewed; Journal article, 2020)
      As the only endemic neotropical parrot to have recently lived in the northern hemisphere, the Carolina parakeet (Conuropsis carolinensis) was an iconic North American bird. The last surviving specimen died in the Cincinnati ...
    • Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features 

      Seki, Ryohei; Li, Caí; Fang, Qi; Hayashi, Shinichi; Egawa, Shiro; Hu, Jiang; Xu, Luohao; Pan, Hailin; Kondo, Mao; Sato, Tomohiko; Matsubara, Haruka; Kamiyama, Namiko; Kitajima, Keiichi; Saito, Daisuke; Liu, Yang; Gilbert, Marcus Thomas Pius; Zhou, Qi; Xu, Xing; Shiroishi, Toshihiko; Irie, Naoki; Tamura, Koji; Zhang, Guojie (Journal article; Peer reviewed, 2017)
      Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One of these magnificent examples is the transition from non-avian dinosaurs to birds that has created numerous ...
    • Genomic adaptations and evolutionary history of the extinct scimitar-toothed cat, Homotherium latidens 

      Barnett, Ross; Westbury, Michael V; Sandoval-Velasco, Marcela; Vieira, Filipe G.; Jeon, Sungwon; Zazula, Grant; Martin, Michael David; Ho, Simon Y.W.; Mather, Niklas; Gopalakrishnan, Shyam; Ramos-Madrigal, Jazmín; de Manuel, Marc; Zepeda-Mendoza, Marie Lisandra; Antunes, Agostinho; Carmona Baez, Aldo; De Cahsan, Binia; Larson, Greger; O'Brien, Stephen J.; Eizirik, Eduardo; Johnson, Warren E.; Koepfli, Klaus-Peter; Wilting, Andreas; Fickel, Jörns; Dalén, Love; Lorenzen, Eline D.; Marques-Bonet, Tomas; Hansen, Anders J.; Zhang, Guojie; Bhak, Jong; Yamaguchi, Nobuyuki; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2020)
      Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1, 2, 3, 4]. They possessed large, saber-form serrated ...
    • High-coverage genomes to elucidate the evolution of penguins 

      Pan, Hailin; Cole, Theresa L.; Bi, Xupeng; Fang, Miaoquan; Zhou, Chengran; Yang, Zhengtao; Ksepka, Daniel T.; Hart, Tom; Bouzat, Juan L.; Argilla, Lisa S.; Bertelsen, Mads F.; Boersma, P. Dee; Bost, Charles-André; Cherel, Yves; Dann, Peter; Fiddaman, Steven R.; Howard, Pauline; Labuschagne, Kim; Mattern, Thomas; Miller, Gary; Parker, Patricia; Phillips, Richard A.; Quillfeldt, Petra; Ryan, Peter G.; Taylor, Helen; Thompson, David R.; Young, Melanie J.; Ellegaard, Martin; Gilbert, Marcus Thomas Pius; Sinding, Mikkel Holger Strander; Pacheco, George; Shepherd, Lara D.; Tennyson, Alan J.D.; Grosser, Stefanie; Kay, Emily; Nupen, Lisa J.; Ellenberg, Ursula; Houston, David M.; Reeve, Andrew Hart; Johnson, Kathryn; Masello, Juan F.; Stracke, Thomas; McKinlay, Bruce; Borboroglu, Pablo García; Zhang, De-Xing; Zhang, Guojie (Peer reviewed; Journal article, 2019)
      Background Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes ...
    • Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus 

      Fotakis, Anna K.; Denham, Sean Dexter; Mackie, Meaghan; Orbegozo, Miren Iraeta; Mylopotamitaki, Dorothea; Gopalakrishnan, Shyam; Sicheritz-Pontén, Thomas; Olsen, Jesper V.; Cappellini, Enrico; Zhang, Guojie; Christophersen, Axel; Gilbert, Thomas; Vågene, Åshild J (Peer reviewed; Journal article, 2020)
      Mineralized dental plaque (calculus) has proven to be an excellent source of ancient biomolecules. Here we present a Mycobacterium leprae genome (6.6-fold), the causative agent of leprosy, recovered via shotgun sequencing ...
    • Pre-extinction demographic stability and genomic signatures of adaptation in the woolly rhinoceros 

      Lord, Edana; Dussex, Nicolas; Kierczak, Marcin; Díez-del-Molino, David; Ryder, Oliver A.; Stanton, David W. G.; Gilbert, Marcus Thomas Pius; Sánchez-Barreiro, Fatima; Zhang, Guojie; Sinding, Mikkel-Holger S.; Lorenzen, Eline D.; Willerslev, Eske; Protopov, Albert; Shidlovskiy, Fedor K.; Fedorov, Sergey; Bocherens, Hervé; Nathan, Senthilvel K.S.S.; Goossens, Benoit; Johannes, van der Plicht; Chan, Yvonne L.; Prost, Stefan; Potapova, Olga R; Kirillova, Irina V.; Lister, Adrian M.; Heintzman, Peter D.; Kapp, Joshua D.; Shapiro, Beth; Vartanyan, Sergey; Götherström, Anders; Dalén, Love (Peer reviewed; Journal article, 2020)
      Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change ...